Biology subjects

Kerscher, A.

Publications and source records attributed to Kerscher, A..

3 recordsLinked to original sources

bioRxiv2026

The lattice scales of grid-cell activity

Grid cells in the rodent medial entorhinal cortex (MEC) form a multi-scale representation of the animals environment and are thought to be a signature of continuous-attractor networks.Experiments suggest that grid scales are discrete and arranged in a geometric progression with constant scale ratios, as predicted by efficient-coding theories that posit that the grid-cell system is optimized for spatial resolution. This normative explanation has been challenged by a developmental theory whereby grid-cell modularity arises from pattern formation in a system with smooth parameter gradients. As a consequence, scale ratios should not be constant, but vary by module. However, as we show here, the experimental data chosen to support this mechanistic theory fail to do so. Publicly available large-scale grid-cell datasets could provide a clear benchmark and further our understanding of the neuronal basis of spatial navigation. We, therefore, reanalyzed such recordings and found that they refute the developmental theory. Instead, the measured scale ratios agree with the geometric-progression hypothesis and set strict bounds for any future grid-cell theory.

neuroscience↗

bioRxiv2025

Acclimation of carbon metabolism to a changing environment across a leaf rosette of Arabidopsis thaliana

O_LIPlants need to efficiently and quickly stabilize photosynthesis and carbon metabolism under changing environmental conditions to prevent irreversible tissue damage C_LIO_LIDifferently developed leaves of Arabidopsis thaliana rosettes are typically homogenized for metabolic analyses which might result in significant over- or underestimation of metabolite dynamics. C_LIO_LIHere, photosynthesis and carbon metabolism were analysed in mature and immature leaves of rosettes of natural Arabidopsis accessions originating from southern and northern Europe. Ambient growth condition at 22 {degrees}C was compared to a combined low temperature/elevated light treatment. C_LIO_LIGradients of Fv/Fm and CO2 assimilation rates across leaf rosettes hinted towards tissue-specific acclimation capacities of photosynthesis and carbon metabolism. C_LIO_LIDynamics of carbohydrates and carboxylic acids were integrated with photosynthetic parameters in a quantitative carbon balance model. Model simulations suggested that mature leaf tissue stabilizes acclimation of carbon metabolism in immature leaf tissue and/or other sink tissue. C_LIO_LIIn conclusion, acclimation capacities of photosynthesis to low temperature and elevated light significantly differ within one leaf rosette of Arabidopsis. This directly affects carbon metabolism which shapes the metabolic acclimation capacity of the whole plant. C_LIO_LIIt is suggested to consider such tissue-specific effects which might otherwise be hidden behind a high variance of experimental data. C_LI

plant biology↗

bioRxiv2021

Visual Clustering of Transcriptomic Data from Primary and Metastatic Tumors: Dependencies and Novel Pitfalls

Personalized Oncology is a rapidly evolving area and offers cancer patients therapy options more specific than ever. Yet, there is still a lack of understanding regarding transcriptomic similarities or differences of metastases and corresponding primary sites. Applying two unsupervised dimension reduction methods (t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation Projection (UMAP)) on three datasets of metastases (n=682 samples) with three different data transformations (unprocessed, log10 as well as log10+1 transformed values), we visualized potential underlying clusters. Additionally, we analyzed two datasets (n=616 samples) containing metastases and primary tumors of one entity, to point out potential familiarities. Using these methods, no tight link between site of resection and cluster formation outcome could be demonstrated, neither for datasets consisting of solely metastasis nor mixed datasets. Instead, dimension reduction methods and data transformation significantly impacted visual clustering results. Our findings strongly suggest data transformation to be considered as another key element in interpretation of visual clustering approaches along with initialization and different parameters. Furthermore, the results indicate only minor transcriptional differences for metastases and corresponding primary tumors.

cancer biology↗